Fluoride (F⁻) is an essential trace element for healthy bones and teeth, yet prolonged intake above recommended levels can cause adverse effects, including dental and skeletal fluorosis. The World Health Organization (WHO) sets a guideline of 1.5 mg L⁻¹ for fluoride in drinking water, with concentrations above this threshold posing chronic health risks, particularly for children and pregnant women. In the urban coastal area of Béjaïa, northern Algeria, groundwater fluoride levels varied significantly between shallow and deep aquifers, with multiple samples exceeding the WHO limit. To evaluate potential health impacts, a human health risk assessment (HHRA) was conducted for three exposure groups—children, women, and men—considering both oral ingestion and dermal contact. Hazard quotients (HQ) for oral exposure indicated that 38.9% of children, 26.7% of women, and 31.1% of men face potential non-carcinogenic risk (HQ > 1), with children showing the highest vulnerability due to lower body weight and higher water intake per unit body mass. Dermal absorption contributed minimally (<5%) to total exposure, confirming ingestion as the primary pathway. Spatial analysis revealed that areas with elevated fluoride were primarily controlled by mineral dissolution and desorption, where extended water–rock interactions under alkaline conditions released fluoride from minerals such as fluorite and apatite. Conversely, zones affected by seawater intrusion or high calcium concentrations showed lower fluoride levels, likely due to precipitation control via fluorite equilibrium. The prevalence of HQ values exceeding unity in a significant fraction of samples underscores the urgent need for mitigation measures and safe water supply strategies in vulnerable neighborhoods. Regular groundwater monitoring, particularly in high-pH, low-calcium regions, is essential to prevent further fluoride accumulation. Public health interventions should focus on awareness campaigns, exposure reduction through treatment or blending (e.g., activated alumina, reverse osmosis), and prioritizing sensitive groups such as school-aged children. Overall, the HHRA demonstrates that fluoride contamination in Béjaïa’s coastal aquifers poses a moderate to high non-carcinogenic risk via oral exposure, highlighting the importance of integrated hydrogeochemical monitoring and targeted public health strategies to safeguard groundwater sustainability and public health in northern Algeria